Is rape in war a serious threat to women, or an exaggeration by cash-hungry aid agencies and scaremongering journalists? With M23 rebels in control of the largest town in eastern Congo, you might assume the former. If so, you will be surprised by a provocative new study from a leading thinktank in Canada.

The report is from the Human Security Report Project at Simon Fraser University and it sets out to demolish the "mainstream narrative" on armed sexual violence. Rape, it says, is not an inevitable product of modern wars – even in countries such as the Democratic Republic of Congo (which has been called "rape capital of the world"). Nor is there evidence that rape is used "strategically" as a weapon of war to break the spirit of civilians. By promoting such myths, says the report, aid agencies and reporters distort policy and make it harder to deal with more insidious evils, such as civilian rape.

Although it's clearly intended to shock, this position is not entirely new or unexpected. It fits into a growing body of research that argues that war is becoming progressively less violent. In The Better Angels of Our Nature, Steven Pinker from Harvard argues that the 20th century was not, in fact, the most deadly in history and that even the second world war was a statistical aberration. Joshua Goldstein, another American academic, devotes a whole chapter in his book Winning the War on War to debunking claims that 5 million civilians may have died in the Congo wars.

But in zeroing in on sexual violence, the Human Security report is going to strike a special nerve. It certainly upset me – partly because our organisation supports rape survivors in eastern Congo (through a Congolese partner), and partly because, as a former journalist and UN official, I have seen how publicity can indeed distort humanitarian aid. One need look no further than the aftermath of the Rwandan genocide, when the international community rushed to feed Hutu genocidaires who fled into eastern Congo. Many of these killers are still living deep in the bush, whence they emerge to rape and kill Congolese villagers.

It is also unnerving to be accused of exploiting rape. We know that nothing sells like sex and violence. Hundreds of NGOs are working on sexual violence in the Kivus, and the media has run some sensational descriptions. Are we all guilty as charged?

Perhaps we were back in 2009, when Hillary Clinton visited the Congo and turned sexual violence into a signature issue of US foreign policy. But no longer. In fact, I doubt if this story still bleeds, let alone leads. I met several rape survivors during a recent trip to the Congo and what they went through was horrific. But it was also numbingly familiar, and even mass rapes rarely make it to the mainstream media. I fear that we are paying for those earlier, overheated descriptions. That sort of publicity is impossible to sustain.

On the ground, agencies that work with rape survivors rarely use "shocking victim narratives, and unsupported generalisations" as the report alleges. In fact, they are often admirably restrained. Our Congolese partner, SOS Femmes en Danger (SOSFED), finds this restrictive and has asked us to publicise names and photos. But this is always done at the request of the women, who feel that publicity is their one way to protest.

Nor do we see any evidence that the UN is pushing a "narrative" of exaggeration. To judge from my own recent meetings in Congo, many UN officials feel that sexual violence is distorting their own work. The UN Population Fund (UNFPA) has handed over data collection to the Congolese government, in order to focus more on maternal mortality. At UN headquarters in New York, meanwhile, the latest report on armed sexual violence by the secretary general, issued on 13 January, was sober and restrained. Ban Ki-moon's first adviser, Margot Wallström, was certainly passionate on the issue, but she resigned in May.

One result of this has been serious under-reporting from eastern Congo. In Fizi territory, one of nine territories in south Kivu, SOSFED took in 138 rape victims between January and August. This was an increase from 2011, but none of these cases were investigated by the UN because Fizi is considered too dangerous. Diplomats never visit, UN aid workers need armed escorts, and UN peacekeepers are afraid of their own shadow. This may explain why the UN's January report only confirmed 167 cases in the whole of south Kivu last year – a ridiculously low figure. Now that UNFPA has pulled out, the data will be even less reliable. The Congolese government will not want to advertise rape by its own troops.

This illustrates one problem with the numbers game. Not only are the facts not getting out from places like the Congo, but the trends can vary from one district to the next. This, however, does not mean that rape is on the decline. In fact the opposite is almost certainly true. Following the M23 rebellion, five armed groups are now fighting each other in the Kivus, and any woman whom they catch in the open will probably get raped if she is from a different ethnic background. This conflict is all about ethnicity, and such acts are no less "strategic" because the rapists are probably not acting under orders. The same is true at the global level. Overall, deaths from war may be in decline, but security is certainly not improving. Look no further than the Middle East.

Perhaps we can all agree on this – there needs to be a more honest attempt to get at the facts. Were this to happen, a new "narrative" about rape in war might indeed emerge and some of it might even be positive. For example, we have found in the Congo that a simple water well can protect women because it reduces their need to travel out alone in search of water where they will be vulnerable to attack. The UN and American Bar Association have funded mobile courts which prosecuted 79 government soldiers for rape last year – a solid achievement that may be imposing some restraint on government troops.

Such a narrative would attract less attention than attacking the motive of aid workers and journalists. But it might be more helpful, coming from a prestigious programme on human security. For those with most at stake, like Congolese women, this is still a very dangerous world.